This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Babbitt group has been a pioneer in identifying enzyme superfamilies, that is, groups of proteins that are distantly evolutionarily related and share nearly undetectable sequence similarity, but that share an architecture and certain aspects of their function. We are comparing structures and observables based on structure among and between families and superfamilies of proteins, with the goal of better understanding how sequence and structure are constrained. We are identifying 3D motifs or active site templates, spatial arrangements of small sets of residues that can be diagnostic of membership in a family or superfamily of proteins. Besides studying known superfamilies, we also wish to characterize sets of related proteins that have not already been well described. Chimera and other sequence and structure analysis tools available locally and on the RBVI web site are employed in this work. We collaborate with the Chimera development team as needed to further the research and facilitate the creation of useful research software. Our initial work on active site templates for the enolase and haloacid dehalogenase superfamilies has been published in Proteins (see below). More recently, our method to automatically discover 3D motifs shared among any group of related proteins has been published in Bioinformatics.